Contains scripts used in "Characterization of caffeine response regulatory variants in vascular endothelial cells" (doi: https://doi.org/10.1101/2022.11.22.517533)
The script used for alignment can be found at https://github.com/cakalita/BiT-STARR-seq/blob/main/alignandprep.sh
DESeq_script.R is the script for differential activity analysis.
To complete ASE and cASE analyses, we first run bitstarr_ASE_analysis.R to obtain individual replicate-level results, and then run manual_calc_meta_analysis_using_quasar_se.R to complete the meta-analysis. Additionally, we filtered our results to remove variants with less data using filter_meta_analysis.R, at which point we calculated the cASE statistics.
To do the enrichment analyses for open chromatin and artery eQTLs, we use the following scripts respectively: open_chromatin_OL.R and chromatin_OL.sh, GTEx_Overlap.R.
For the motif analysis, PWM_Scan.sh is the script used to scan for motifs and motif_proptest.R is the script used to complete the statistical test.
cASE_statistics_working_back_from_INTACT.R is the script used to view the overlap between our results and the fine-mapped artery eQTLs and is also the script used to link our INTACT results with our cASE results.